Exploring Freshwater Biodiversity Using eDNA

Biodiversity is disappearing faster than at any time in recorded history. Freshwater species are among the most vulnerable to extinction, making it imperative to understand freshwater biodiversity. Logistical challenges and financial costs make freshwater biodiversity monitoring an increasingly overwhelming task, especially as demand for biodiversity information outpaces funding and available taxonomic expertise.

Brooke Penaluna wades in to take a water sample for eDNA testing to detect aquatic species. Photo by Loretta Ellenburg USDA Forest Service.

Research Description

Environmental DNA (eDNA) metabarcoding is increasingly used as an alternate method for measuring biodiversity, as DNA left behind by individuals in the water can be used for taxonomic identification (e.g., family, genus, and species). Typically, eDNA metabarcoding uses the polymerase chain reaction (PCR) to amplify short, taxonomically informative genomic regions (“DNA barcodes”) from samples. Amplified DNA is then sequenced, and the sequences are classified to reveal a breadth of taxonomic and genetic diversity in the DNA present in each water sample.

Key Findings

We are applying eDNA metabarcoding to waterways throughout the Pacific Northwest of the continental United States to identify freshwater biodiversity and population genetic diversity, which will help managers meet multiple management objectives. For example, we identified 878 taxa at Fall Creek in the Alsea River basin in the Oregon Coast Range (Hauck et al. 2019). DNA sequences were obtained for multiple targeted groups, including sequences from fish (Actinopteri, Petromyzontidae; 50.1 percent of sequences), pathogenic oomycetes (water molds, 21.3 percent), arthropods (classes Insecta, Decapoda; 16.5 percent), and apicomplexan parasites (3.8 percent), and even amphibians and beaver (less than 1 percent each). The resulting genomic databases can be used to track the magnitude and distribution of genetic diversity in managed species (Weitemier et al. 2021). They can also be used to determine the presence and diversity of forest pathogens. These approaches provide science-based, region-specific biodiversity information that facilitate science-informed decisions.

eDNA filters from water sampling in Fall Creek in the Alsea River basin, Oregon. Photo by Brooke Penaluna, USDA Forest Service.

Mitochondrial haplotypes of coastal cutthroat trout using the ND2 locus (gene). Colored pie charts represent reads, with pie sizes proportional to the number of reads observed (summed across replicates), given by the scale in the lower right. Colored pie slices represent unique haplotypes (inheritable DNA variants). White squares mark sampling locations where trout were not captured (Weitemier et al. 2021).

 Management Implications

• Our work broadens the scope of eDNA information by allowing for data-driven prioritization of multiple aquatic species, including common, endangered, rare, and cryptic species, to inform conservation actions and forest health objectives.
• The ability to better detect freshwater biodiversity is a critical step toward managing for the persistence of genetic diversity within populations and for diversity of species across riverscapes.
• As human activities continue to affect aquatic habitats and their populations, continued genetic monitoring of multiple aquatic species is necessary to assess the direction and extent of those impacts and provide critical information to managers tasked with maintaining healthy ecosystems.